QC APP

Introduction

Welcome to your [QCPName] Quality Control Analysis Report! We are pleased to present to you a visual QC summary of your dataset. Representing high-dimensional omics data using plots helps us view large amounts of information at once to identifying patterns and trends across your samples and datasets. The "[QCP Name]" package monitors metrics based on the input datasets provided. For any concerns about or suggestions to improve this report, let the team know at GroupHeartBioinformaticsSupport@cshs.org, and we will consider your feedback. We are happy to support your computational needs.

The report is divided into 2 tabs:

  • ID-Free - When a mzML directory is provided as input, ID-Free Tab is populated with plots from ID-Free parameters extracted from your mzML files.
  • ID-Based - When a protein, peptide or precursor level intensity file is provided, ID-based Tab will be populated with ID-based parameters extracted from your quantified input.

ID-Based Metrics

The following metrics have been calculated and derived from the input search results that were provided. Given input thresholds have been applied and if grouping file was provided, groupwise comparison has also been performed.


Protein Quantification

Number of proteins identified from each sample. Any sample not meeting the threshold could indicate an issue within sample preparation or digestion protocols.

Precursor Quantification

Number of precursors identified from each sample. Any sample not meeting the threshold could indicate an issue within sample preparation or digestion protocols.


Intensity CV% Cumulative Frequency

Cumulative Frequency % of calculated CV% across all samples

Percentage of Proteins Under CV%

Intensity CV% across samples within each group is calculated. Threshold is set to 70.0% of proteins under 40.0 CV%

Percentage of Precursors Under CV%

Intensity CV% across samples within each group is calculated. Threshold is set to 70.0% of precursors under 40.0 CV%


PCA for Protein Intensities

PCA plot from protein intensities across provided groups. If any grouping/clustering is observed, please check for batch effects across the provided groups.

PCA for Precursor Intensities

PCA plot from precursor intensities across provided groups. If any grouping/clustering is observed, please check for batch effects across the provided groups.


Common Precursor TIC

The Total Ion Current here is calculated from intensities of common precursors found in all samples. Any inconsistent patterns could indicate problems in sample preparation.

Common Precursor TIC Group CV%

Common Precursor TIC CV% calculated from intensities of common precursors within each provided group. A CV% higher than the set threshold of 40.0 indicates an inconsistency within the samples of the group.


Percent Miscleavage

Total Number of 0 miscleaved peptides found in each sample. If the percentage of 0 miscleaved peptides is under the miscleavage threshold value of 80.0%, this could indicate issues with sample preparation and digestion protocols.